As a result of funding shortfalls for the Vietnam War that resulted in the closure of numerous stateside air force bases and naval air stations, Suffolk County AFB deactivated in 1969 and the military installation was again transferred to the Suffolk County government for use as a civilian airport.

The book The Perfect Storm and the film by the same name detail the crash of one of the 106th's HH-60G Pave Hawk rescue helicopters while conducting civilian search and rescue operations from the airport during the 1991 Perfect Storm.